Preheat oven to 350℉ and line a sheet pan with parchment paper. Set aside.
Place the flour, brown sugar, salt, and butter into a food processor and pulse to break up the butter. Next, add the cottage cheese and pulse to combine. It should look crumbly, but not wet.
Turn the processor on and slowly add cold water 1 tablespoon at a time. Once a ball has started to form you can stop.
Transfer the dough to a floured work surface and divide into two equal portions. Roll out one piece to 12x12 inches and then transfer it to the lined sheet pan. Set aside.
Mix the brown sugar, cinnamon, and protein powder in a small bowl.
Spread the brown sugar mix on top of the dough, leaving about ½ inch around the border to crimp the edges. Set aside.*
Roll out the remaining dough and place on top of the brown sugar mixture. Using a fork, crimp the edges to seal. Then, poke the fork into the top of the pop tart to stop air bubbles.
Bake for 25-30 minutes at 350℉.
While the pop tart is baking, make the glaze. Place the powdered sugar, almond milk, and vanilla in a bowl and mix to combine. Cover with plastic wrap to stop a film from forming on top.
Remove the pop tart from the oven and allow it to cool for 15-20 minutes before topping it with the glaze. Slice into equal size squares or rectangles.